Periodic Reporting for period 2 - VIROME (Shaping of long term innate immunity by viral education of bone marrow monocytes) Reporting period: 2021-07-01 to 2022-12-31 Summary of the context and overall objectives of the project The recent pandemic has highlighted the heterogeneity of immune responses between individuals. Environmental factors are key drivers of immune variations between individuals. Among these factors, symbiotic and pathogenic microbes are major determinants that play fundamental roles in shaping immunity. While frequently underestimated, immune imprinting by viruses is responsible for significant variation in disease susceptibility. There is ample evidence shows that a history of infections trains the innate immune system for the long term. Among the cells that are trained, monocytes are highly heterogeneous and participate in essential biological processes such as anti-microbial activity, immunomodulation or macrophage-niche replenishment. The overall goal of this ERC project is to understand how and where monocyte development and function are educated by symbiotic (Murid herpesvirus 4) or pathogenic (Pneumonia Virus of Mice) viruses and with which potential outcomes for long-term immunity. To this end, we have devised three main aims. First, we characterize the monocytes and their progenitors by classical immunophenotyping, functional assays and unbiased single-cell RNA-seq in combination with ATAC-seq, to investigate in-depth how and where viruses shape monocytes and monocyte-derived cells (WP1). Second, the molecular mechanisms underlying monocyte priming after infections are being evaluated. In particular, we are investigating the role of bone marrow CD169+ macrophages in early monocyte priming (WP2). Third, the consequences of virus-driven monocyte training are being studied in the context of the primary viral infections, but also in the context of several heterologous immune responses (WP3). This research may provide evidence that viral education of bone marrow monocytes shapes long-term innate immunity. Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far WP1/ Immunoprofiling of virus imprinted-monocytesMuHV-4 and PVM models have been used to perform a high resolution phenotypic characterization of virus-imprinted monocytes. Indeed, monocytes isolated from bone marrow, blood and lung of mock or virus-infected mice have been analysed by flow cytometry at different times post-infection, as well as monocyte progenitors. This classical immunophenotyping has revealed specific functional properties and distinct activation states between the two models of infection. In addition, a transcriptomic profiling by single-cell RNA sequencing has been done in the context of MuHV-4 acute infection revealing key regulatory features. Furthermore, we demonstrated a variable long-term contribution of monocytes to the macrophage alveolar niche for a similar level of niche depletion. This result contradicts the niche hypothesis (arguing that niche accessibility is the major factor explaining monocyte engraftment) and shows that other intrinsic or extrinsic factors, may influence this phenomenon.WP2: Investigation of the functional outcomes of monocyte imprinting for the host immunity.3.1. Investigation of the consequences of monocyte imprinting for the primary anti-viral responseHere, we studied the importance of monocytes for MuHV-4 lifecycle. As stated above, monocytes are pleiotropic cells contributing to the overall orchestration of immunity. Understanding the balance between pro-inflammatory and immunomodulatory pathways triggered by monocytes upon viral infections is of major importance since mechanisms underlying deleterious inflammation induced by highly pathogenic respiratory viruses, are not well known yet. Most surprisingly, we have highlighted the essential role of monocytes recruited to the airways in controlling inflammation, as the absence of these monocytes transforms an asymptomatic infection into a lethal immunopathology. In particular, we highlighted the key importance of the PD-L1/PD-1 regulatory axis to control the cytotoxic properties of lung-infiltrating CD4 T cells and to prevent tissue damage related to anarchic degranulation of these cells. This study was published in Science Immunology (DOI: 10.1126/sciimmunol.abn3240). 3.2. Investigation of the consequences of monocyte imprinting for long-term lung immunityHere we investigate how viral infections affect the alveolar landscape and what mechanisms determine the long-term persistence of monocyte-derived alveolar macrophages. Indeed, while alveolar niche depletion is a common consequence to different inflammatory insults, only some specific contexts allow the lasting engraftment of monocyte-derived cells. Using partial bone marrow chimeras and complementary fate-mapping models, we observed significant differences in the alveolar niche replenishment during distinct viral infections. Viral imprinting of the alveolar landscape has further consequences on heterologous responses such as the development of allergic asthma. Thus, we demonstrated that MuHV-4 protects against the development of allergic asthma by replacing alveolar macrophages with regulatory monocytes. As a direct extension of this initial study, here we investigated the cell-cell interaction between alveolar macrophages and lung-resident niche cells, and discovered a key role for type 2 innate lymphoid cells in alveolar macrophage identity and function.(Study currently in revision in Science Immunology). Besides, we also highlighted the protection conferred by gammaherpesvirus imprinting against unrelated viral infections. In particular, we revealed that MuHV-4 infection licenses CD8 T cells to protect the host from pneumovirus-induced immunopathologies. (Publication accepted in March 2020 in Mucosal Immunology, https://doi.org/10.1038/s41385-020-0293-7). In the light of these results, we have next investigated whether the history of viral infection may affect the quality of the anti-tumour cellular response in the lung over the long term. Interestingly, we have highlighted that distinct respiratory viruses have a major and opposite influence on the properties of cytotoxic lymphocytes, ranging from terminal anergy to beneficial activation. While the underlying mechanisms are still under investigation, this study has been presented at several international meetings ('Translational Immunology VIB 202; Belgium society for Virology annual meeting; Early life type 2 immunity, ULiege, Recent insights into immunology-oncology VIB 2022) and has been awarded two renowned scientific prizes (GSK-Basic Sciences, Nature Reviews Cancer-poster prize 3.3. Investigation of the consequences of monocyte imprinting for long-term lung immunityBeyond the respiratory tract, monocyte viral imprinting could shape immune response organs that are not directly targeted by the primary infections. In particular, since monocytes constantly contribute to the pool of intestinal macrophages, we are interested in studying importance of the history of viral infection for the development of individual susceptibility to inflammatory intestinal diseases as well as the potential underlying mechanisms.WP3: Investigation of the mechanisms underlying the initial priming of monocytesIn this part of the project, we investigate the initiating steps leading to monocyte training. In particular, we are studying the role of resident CD169+ bone marrow macrophages in monocyte early education during viral infection. Interestingly, we observed important phenotypic alterations of these bone marrow macrophages after infection such as overexpression of MHCI and MHCII molecules but also increased expression of cytokines and chemokines, suggesting the existence of a biological crosstalk between these macrophages and other immune cells. Importantly, by using CD169 DTR transgenic mice allowing the inducible depletion of these macrophages, we observed the ablation of bone marrow CD169+ macrophages skews the monocyte phenotype towards an inflammatory profile, associated with viral disease exacerbation. RNA sequencing of those bone marrow macrophages has been done and are currently under analysis. These data will improve our understanding of the biology of bone marrow CD169+ macrophages upon viral infection and will also designed relevant target useful to generate a new transgenic mouse model allowing a more specific depletion of these cells. Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far) The results generated by this project could reveal new insights in the mechanisms underlying the long-term training of monocytes and monocyte-derived cells. Importantly, it could provide the proof of concept that viral infection induces major training effects on monocyte populations. In future, the investigations could be extended to other organs and other inflammatory challenges. Such general understanding could be useful for the development of better vaccines and therapeutics.